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PubMed1994

Molecular dynamics simulation of a hydrated phospholipid bilayer.

A hydrated bilayer of the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) has been studied in the course of a molecular dynamics simulation. Comparison of the simulation results with experiment indicates that generally the two agree well. Data are presented concerning all the major system regions, including the hydrocarbon chains, the glycerol region, the lipid headgroups and the hydrating water molecules. The simulations suggest that this model can be extended to the study of more complex systems of greater biochemical interest, such as membrane bound proteins.

Computer Simulation↗
PubMed2005

Molecular dynamics simulations indicate a possible role of parallel beta-helices in seeded aggregation of poly-Gln.

The molecular structures of amyloid fibers characterizing neurodegenerative diseases such as Huntington's or transmissible spongiform encephalopathies are unknown. Recently, x-ray diffraction patterns of poly-Gln fibers and electron microscopy images of two-dimensional crystals formed from building blocks of prion rods have suggested that the corresponding amyloid fibers are generated by the aggregation of parallel beta-helices. To explore this intriguing concept, we study the stability of small beta-helices in aqueous solution by molecular dynamics simulations. In particular, for the Huntington aggregation nucleus, which is thought to be formed of poly-Gln polymers, we show that three-coiled beta-helices are unstable at the suggested circular geometries and stable at a triangular shape with 18 residues per coil. Moreover, we demonstrate that individually unstable two-coiled triangular poly-Gln beta-helices become stabilized upon dimerization, suggesting that seeded aggregation of Huntington amyloids requires dimers of at least 36 Gln repeats (or monomers of approximately 54 Gln) for the formation of sufficiently stable aggregation nuclei. An analysis of our results and of sequences occurring in native beta-helices leads us to the proposal of a revised model for the PrP(Sc) aggregation nucleus.

Amino Acid Motifs↗
PubMed2004

Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: effect of protonation of histidine residues.

The role of acidic pH in the conversion of human prion protein to the pathogenic isoform is investigated by means of molecular dynamics simulations, focusing the attention on the effect of protonation of histidine residues on the conformational behavior of human PrPC globular domain. Our simulations reveal a significant loss of alpha-helix content under mildly acidic conditions, due to destructuration of the C-terminal part of HB (thus suggesting a possible involvement of HB into the conformational transition leading to the pathogenic isoform) and a transient lengthening of the native beta-sheet. Protonation of His-187 and His-155 seems to be crucial for the onset of the conformational rearrangement. This finding can be related to the existence of a pathogenic mutation, H187R, which is associated with GSS syndrome. Finally, the relevance of our results for the location of a Cu2+-binding pocket in the C-terminal part of the prion is discussed.

Computer Simulation↗
PubMed1994

Molecular distributions in interphases: statistical mechanical theory combined with molecular dynamics simulation of a model lipid bilayer.

A mean-field statistical mechanical theory has been developed to describe molecular distributions in interphases. The excluded volume interaction has been modeled in terms of a reversible work that is required to create a cavity of the solute size against a pressure tensor exerted by the surrounding interphase molecules. The free energy change associated with this compression process includes the configuration entropy as well as the change in conformational energy of the surrounding chain molecules. The lateral pressure profile in a model lipid bilayer (30.5 A2/chain molecule) has been calculated as a function of depth in the bilayer interior by molecular dynamics simulation. The lateral pressure has a plateau value of 309 +/- 48 bar in the highly ordered region and decreases abruptly in the center of the bilayer. Model calculations have shown that for solute molecules with ellipsoidal symmetry, the orientational order increases with the ratio of the long to short molecular axes at a given solute volume and increases with solute volume at a given axial ratio, in accordance with recent experimental data. Increased lateral pressure (p perpendicular) results in higher local order and exclusion of solute from the interphase, in parallel with the effect of surface density on the partitioning and local order. The logarithm of the interphase/water partition coefficient for spherical solutes decreases linearly with solute volume. This is also an excellent approximation for elongated solutes because of the relatively weak dependence of solute partitioning on molecular shape. The slope is equal to (2p perpendicular - p parallel)/3KBT, where p parallel is the normal pressure component, and different from that predicted by the mean-field lattice theory. Finally, the lattice theory has been extended herein to incorporate an additional constraint on chain packing in the interphase and to account for the effect of solute size on partitioning.

Biomechanical Phenomena↗
PubMed2006

Molecular dynamics simulation of interactions in glycolytic enzymes.

Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae, have been chosen to detect complex formation and possible channeling, using molecular dynamics simulation. The enzymes were separated by 10 angstroms distance and placed in a water-filled box of size 173 x 173 x 173 angstroms. Three different orientations have been investigated. The two initial 3-phosphoglycerate substrate molecules near the active centers of the initial structure of PGM have been replaced with final product (2-phosphoglycerate) molecules, and 150 mM NaCl together with three Mg2+ ions have been added to the system to observe post-catalytic activity under near-physiological conditions. Analysis of interaction energies and conformation changes for 3 nsec simulation indicates that PGM and enolase do show binding affinity between their near active regions, which is necessary for channeling to occur. Interaction of the C-terminal residues Ala239 and Val240 of PGM (which partially "cap" the 2-phosphoglycerate) with enolase also favors the existence of channeling.

Binding Sites↗
PubMed2002

Membrane structure of the human immunodeficiency virus gp41 fusion domain by molecular dynamics simulation.

The structures of the 16-residue fusion domain (or fusion peptide, FP) of the human immunodeficiency virus gp41 fusion protein, two of its mutants, and a shortened peptide (5-16) were studied by molecular dynamics simulation in an explicit palmitoyloleoylphosphoethanolamine bilayer. The simulations showed that the active wild-type FP inserts into the bilayer approximately 44 degrees +/- 6 degrees with respect to the bilayer normal, whereas the inactive V2E and L9R mutants and the inactive 5 to 16 fragment lie on the bilayer surface. This is the first demonstration by explicit molecular dynamics of the oblique insertion of the fusion domain into lipid bilayers, and provides correlation between the mode of insertion and the fusogenic activity of these peptides. The membrane structure of the wild-type FP is remarkably similar to that of the influenza HA(2) FP as determined by nuclear magnetic resonance and electron spin resistance power saturation. The secondary structures of the wild-type FP and the two inactive mutants are quite similar, indicating that the secondary structure of this fusion domain plays little or no role in affecting the fusogenic activity of the fusion peptide. The insertion of the wild-type FP increases the thickness of the interfacial area of the bilayer by disrupting the hydrocarbon chains and extending the interfacial area toward the head group region, an effect that was not observed in the inactive FPs.

Cell Membrane↗
PubMed2000

The Correlation Functions of a Suspension of Large Particles in Amorphous Polybutadiene: A Molecular Dynamics Simulation Study.

The correlation functions of a suspension of Lennard-Jones large particles in a model 1,4-cis-polybutadiene solvent have been investigated by molecular dynamics simulations. We present the effects of temperature, the degree of polymerization, and the solvent/large particle density on the effective interactions between the large particles and the solvent. It is found that as the temperature increases, the structure between solvent-solvent, solvent-large particle, and large-large particle decreases. Additionally, as the bulk density or the chain length is increased, the attractive part of the large-large interaction becomes weaker and small. We believe that in part, this is due to the polymer having collapsed onto itself and entangling the large particles and lessening their interaction until they are actually in contact. Increasing the length of the polymer also entangles the large particles. However, we believe that this may be a general feature that is a characteristic of a polymer solvent containing macroscopically large colloidal particles even though entanglement should be of less significance. Copyright 2000 Academic Press.

Journal Article↗
PubMed2005

Ab initio molecular dynamics simulations of the oxygen reduction reaction on a Pt(111) surface in the presence of hydrated hydronium (H3O)(+)(H2O)2: direct or series pathway?

Car-Parrinello molecular dynamics simulations have been performed to investigate the oxygen reduction reaction (ORR) on a Pt(111) surface at 350 K. By progressive loading of (H3O)(+)(H2O)(2,3) + e- into a simulation cell containing a Pt slab and O2 for the first reduction step, and either products or intermediate species for the subsequent reduction steps, the detailed mechanisms of the ORR are well illustrated via monitoring MD trajectories and analyzing Kohn-Sham electronic energies. A proton transfer is found to be involved in the first reduction step; depending on the initial proton-oxygen distance, on the degree of proton hydration, and on the surface charge, such transfer may take place either earlier or later than the O2 chemisorption, in all cases forming an adsorbed end-on complex H-O-O*. Decomposition of H-O-O* takes place with a rather small barrier, after a short lifetime of approximately 0.15 ps, yielding coadsorbed oxygen and hydroxyl (O + HO*). Formation of the one-end adsorbed hydrogen peroxide, HOO*H, is observed via the reduction of H-O-O*, which suggests that the ORR may also proceed via HOO*H, i.e., a series pathway. However, HOO*H readily dissociates homolytically into two coadsorbed hydroxyls (HO* + HO*) rather than forming a dual adsorbed HOOH. Along the direct pathway, the reduction of H-O* + O* yields two possible products, O* + H2O* and HO* + HO*. Of the three intermediates from the second electron-transfer step, HOO*H from the series pathway has the highest energy, followed by O* + H2O* and HO* + HO* from the direct pathway. It is therefore theoretically validated that the O2 reduction on a Pt surface may proceed via a parallel pathway, the direct and series occurring simultaneously, with the direct as the dominant step.

Journal Article↗
PubMed2006

Ab initio molecular dynamics simulations of elimination reactions in water solution: exploring the borderline region between the E1cb and E2 reaction mechanisms.

We report a theoretical study, based on ab initio molecular dynamics simulations in water solution, of the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Recent theoretical and experimental evidence points toward the lack of a net distinction between the E1cb and E2 reaction paths, which seem to merge smoothly into each other in these borderline cases (Alunni, S.; De Angelis, F.; Ottavi, L.; Papavasileiou, M.; Tarantelli, F. J. Am.Chem. Soc. 2005, 127, 15151-15160). In this study, we explore the dynamics on the potential energy surface for the reaction of 2-(2-fluoroethyl)-1-methyl pyridinium with OH- by means of Car-Parrinello simulations in water solution. Our results indicate that the reaction mechanism effectively evolves through the potential energy region of the carbanion: the carbon-fluoride bond breaks only after the carbon-hydrogen bond, confirming the conclusions of a recently reported study of the potential energy surface for this system.

Journal Article↗
PubMed2004

Molecular dynamics simulation of water in a contact with an iron pyrite FeS2 surface.

A strong adsorption of the water molecules to the pyrite surface is shown by a molecular dynamic simulation of the water-iron pyrite FeS2 interface. Water molecules closest to the pyrite surface are bound by an electrostatic interaction to the iron atoms in grooves running parallel to one of the crystal axes. The grooves are about two atoms wide and are directed along 010 for the (001) surface. The position of the water-surface potential minimum and the energy of adsorption were determined by optimization for a single water molecule at the interface. At room temperature and normal density there are altogether three distinguishable layers of water above the surface. One is associated with the groove: one with H bonding to the sulphur atoms comprising the ridges separating the grooves, and the third with the soft wall boundary between the absorbed water layers and bulk region of water. Simulations were also used to explore the effect of a temperature range significant for geophysical studies.

Journal Article↗
PubMed1985

Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions.

We present the results of molecular dynamics simulations on d(C-G-C-G-A) X d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the two simulations are similar, but the simulation with counterions does give an average helix repeat, tilt, and twist in better agreement with those found in the x-ray structure of d(C-G-C-G-A-A-T-T-C-G-C-G)2. The average sugar pucker phases and amplitudes are in qualitative agreement with those found in NMR studies of double-helical DNA, and a number of examples of sugar repuckering from C2' endo to C3' endo carbon conformations in the sugar ring are found. The hydrogen bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.

Magnetic Resonance Spectroscopy↗
PubMed2004

Ab initio molecular-dynamics simulations of short-range order in liquid Al80Mn20 and Al80Ni20 alloys.

Atomic structures of liquid Al80Mn20 and Al80Ni20 have been calculated by first-principles molecular-dynamics simulations. For both liquid alloys, the local structure is characterized by a strong Al-TM (transition metal) affinity, which leads to a well-pronounced chemical short-range order. However, we show that the occurrence of magnetic moments localized on Mn atoms plays a key role in determining the short-range arrangement of Mn atoms which is also interpreted on the basis of the local fivefold symmetry.

Journal Article↗
PubMed1988

Molecular dynamics simulation of despentapeptide insulin in a crystalline environment.

Despentapeptide insulin (DPI), an analogue of insulin, is the only analogue of insulin existing as a monomer in crystalline form so far discovered. A 31 picosecond molecular dynamics simulation of DPI was carried out in the unit cell that includes four DPI molecules, 398 water molecules, four Cd2+, eight Na+ and four Cl-. The molecular dynamics results were compared with the available X-ray structure in terms of atomic positions, backbone dihedral angles, hydrogen bonds and positional fluctuations. Good agreement was found between the molecular dynamics results and the X-ray data. The largest root-mean-square fluctuations were observed at the N-terminal part of the B chain. This fits with the experimental observation.

Amino Acid Sequence↗
PubMed2006

Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. a molecular dynamics simulation study.

Understanding the lipid phase transition of lipid bilayers is of great interest from biophysical, physicochemical, and technological points of view. With the aim of elucidating the structural changes that take place in a DPPC phospholipid bilayer induced by an external isotropic surface pressure, five computer simulations were carried out in a range from 0.1 to 40 mN/m. Molecular dynamics simulations provided insight into the structural changes that took place in the lipid structure. It was seen that low pressures ranging from 0.1 to 1 mN/m had hardly any effect on the structure, electrical properties, or hydration of the lipid bilayer. However, for pressures above 40 mN/m, there was a sharp change in the lipid-lipid interactions, hydrocarbon lipid fluidity, and electrostatic potential, corresponding to the mesomorphic transition from a liquid crystalline state (L(alpha)) to its gel state (P'(beta)). The head lipid orientation remained almost unaltered, parallel to the lipid layer, as the surface pressure was increased, although a noticeable change in its angular distribution function was evident with the phase transition.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1990

Molecular dynamics simulation provides a possible structure for substance P-like peptides in aqueous solution.

A hypothetical conformation of the undecapeptide Substance P in aqueous solution is generated by molecular dynamics simulation for 284 ps. The conformation takes explicit solvent interactions into account as well as entropic effects to the extent that phase space is sampled in simulation. The initial conformation is taken from energy minimization studies and modified. In spite of fluctuations through 180 degrees in some backbone dihedral angles, the peptide settles with all backbone dihedrals within +/- 60 degrees from the initial values. In 130 ps, the radius of gyration decreases from 6.2 A to 5.5 A, whereas only fluctuation (+/- .2 A) is observed during the last 150 ps. The root-mean-square deviation at optimal superposition for a pair of conformations from the last 150 ps is 0.6 A, based on backbone atoms. The final structure is close-knit, nearly globular, and stabilized by several long-lived hydrogen bonds. The simulation conformation agrees with the scarce experimental data including a large number of structure-activity relationships. Thus, the simulation conformation is a likely candidate for one of the several conformations, the existence of which has been deduced from nuclear magnetic resonance data. Simulation results and experimental modification studies suggest that Phe 8 and Leu 10 are involved in the primary binding of SP to its receptors.

Amino Acid Sequence↗
PubMed2003

Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.8-2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions g(r) of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1998

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints.

The folding of the potato carboxypeptidase inhibitor (PCI) from partially unfolded conformations by the introduction of native disulfide bond constraints was studied by molecular dynamics simulations in explicit solvent. PCI consists of a globular core (Cys8 to Cys34), two flexible terminal regions (Glu1 to Ile7 and Glu35 to Gly39) and three loop regions characteristic of the family of proteins known as knottins. To generate unfolded conformations, two high temperature (600 K) simulations were performed; one with the native disulfide bonds intact (N600), and one with the disulfide bonds broken (ND600). For comparison purposes, two simulations at 300 K were done; one with the native disulfide bonds (N300), and one with the disulfide bonds broken (ND300). The N300 simulation reached an energetic equilibrium within a few picoseconds and maintained a stable structure during the 500 ps simulation. The three other simulations led to partial unfolding. The largest changes were observed in ND600 simulation with an rms deviation of over 5 A and radius of gyration 12.5% larger than the crystal structure value. Six structures from the ND600 simulation and one from the N600 simulation were used as starting structures for nine refolding simulations with somewhat different protocols for reforming the native disulfide bonds; in all cases the disulfides were reformed at 600 K and the temperature was decreased to 300 K for equilibration of the folded structures. Except for one structure that was significantly misfolded (final rms of 6.64 A with respect to N300), the other folding simulations recovered the native simulation structure (N300) to within rms differences ranging from 1.8 to 3.2 A for the main-chain of the core, relative to the N300, the X-ray and the NMR structures. Of particular interest is the internal and overall refolding behavior of the three loop regions. The more unfolded starting structures led to smaller rms values for the folded structures. Several energetic and solvation models were used to evaluate the X-ray, NMR, N300 and refolded structures. Although most models can distinguish the X-ray, NMR and N300 from the refolded structures, there is no correlation between the rms values of the latter and their estimated stability. Implications of the present results for protein folding by simulations and database search methods are discussed.

Computer Simulation↗
PubMed2006

Insight into the inhibition of human choline kinase: homology modeling and molecular dynamics simulations.

A homology model of human choline kinase (CK-alpha) based on the X-ray crystallographic structure of C. elegans choline kinase (CKA-2) is presented. Molecular dynamics simulations performed on CK-alpha confirm the quality of the model, and also support the putative ATP and choline binding sites. A good correlation between the MD results and reported CKA-2 mutagenesis assays has been found for the main residues involved in catalytic activity. Preliminary docking studies performed on the CK-alpha model indicate that inhibitors can bind to the binding sites of both substrates (ATP and choline). A possible reason for inhibition of choline kinase by Ca(2+) ion is also proposed.

Amino Acid Sequence↗